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Lossy Compression of Quality Values in Sequencing Data

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1958-1969页

作者： Morales, Veronica Suaste Houghten, Sheridan CONABIO Mexico City 14010 DF Mexico Brock Univ Dept Comp Sci St Catharines ON L2S 3A1 Canada

the dropping cost of sequencing human dna has allowed for fast development of several projects around the world generating huge amounts of dna sequencing data. this deluge of data has run up against limited storage space, a problem that researchers are trying to solve through compression techniques. In this study we address the compression of SAM files, the standard output files for dna alignment. We specifically study lossy compression techniques used for quality values reported in the SAM file and analyze the impact of such lossy techniques on the CRAM format. We present a series of experiments using a data set corresponding to individual NA12878 with three different fold coverages. We introduce a new lossy model, dynamic binning, and compare its performance to other lossy techniques, namely Illumina binning, LEON and QVZ. We analyze the compression ratio when using CRAM and also study the impact of the lossy techniques on SNP calling. Our results show that lossy techniques allow a better CRAM compression ratio. Furthermore, we show that SNP calling performance is not negatively affected and may even be boosted.

关键词： Sequential analysis dna Standards Genomics Bioinformatics Data models Compression algorithms Compression next-generation sequencing quality values SNP calling performance

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FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for dna-Sequences

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1924-1936页

作者： Medhat, Belal Shawish, Ahmed British Univ Egypt Dept Comp Sci Fac Informat & Comp Sci Cairo 11837 Egypt German Univ Cairo Dept Comp Sci Fac Media Engn & Technol Cairo 11837 Egypt Arab Open Univ Fac Comp Studies Headquarters Kuwait Kuwait Ain Shams Univ Fac Comp & Informat Sci Cairo 11566 Egypt

this paper introduces a novel alignment-free sequence analysis methodology. Its main idea is based on introducing a new representation of the dna-Sequence. this representation breaks the dependency between the dna bases that exist in the traditional string presentation. We called it the Four-Lists-Representation (FLR). Based on the FLR, a series of revolutionary algorithms for searching, map-discovery, similarity-score analysis, and similarity-visualization have been developed. they are combined in what we call the FLR Methodology. the paper also studies most of the available similarity analysis techniques in a comprehensive state-of-art review. the conducted extensive simulation and theoretical studies confirm the outperformance of the whole set of FLR-based algorithms in terms of speed and memory consumption in comparison to a long list of available similarity analysis algorithms. the ability to provide a similarity-map, similarity-score, and similarity-graph as a set of evidence-based rationales makes the quality of results provided by the proposed methodology presents a new edge in this field and promises a new area of genome-based research.

关键词： dna Sequences Genomics Bioinformatics Acceleration Organisms Diseases Sequence analysis similarity-score similarity analysis similarity measurements FLR alignment-free sequence analysis

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A Low-drift Extended-Gate Field Effect Transistor (EGFET) with Differential Amplifier for Cordyceps Sinensis dna Detection Optimized by gm/ID theory 15

A Low-drift Extended-Gate Field Effect Transistor (EGFET) wi...

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15th IEEE international conference on Nano/Micro Engineered and molecular System, NEMS 2020

作者： Xu, Yifan Tavakkoli, Hadi Xu, Jingting Lee, Yi-Kuen Hong Kong University of Science and Technology Department of Chemical and Biological Engineering China

ISBN: (纸本)9781728172309

An extended-gate field effect transistor (EGFET) integrated with a differential MOSFET amplifier and an open-source Arduino Yun MCU system was realized for detection of Cordyceps Sinensis dna molecules. A gold microelectrode chip coated with a single-stranded dna probe, as the extended gate was fabricated by MEMS fabrication processes. the differential MOSFET amplifier and additional coating of alkyl-thiol reduced the drifting by one order of magnitude. Moreover, generalized gm/ID theory was used to study the optimized working regime of the EGFET sensor. the highest electric-electrochemical sensitivity could be achieved in the Moderate Inversion (MI) regime. the sensitivity and limit of detection (LOD) of the EGFET sensor were obtained to be 13.85mV/dec and 10nM, respectively. this low-cost low-drift EGFET sensor system is promising for Internet of Living things in the near future. © 2020 IEEE.

关键词： dna

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dna Sequence Alignment Using Dynamic programming 3rd

DNA Sequence Alignment Using Dynamic Programming

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3rd international conference on Intelligent computing and Communication (ICICC)

作者： Singh, Niharika Rajput, Gaurav Dixit, Yash Sehgal, Aastha Univ Petr & Energy Studies Sch CS Dehra Dun Uttarakhand India GL Bajaj Inst Technol & Management Dept CS&E Greater Noida Utter Pradesh India UPES Sch Comp Sci Dept Informat Dehra Dun Uttarakhand India

ISBN: (纸本)9789811510847;9789811510830

In today's time, molecular Science is increasingly dependent on Software Engineering Calculations in the department of Research and Development. Aligning sequences of dna, RNA is becoming a major part of present-day natural sciences. A hereditary database holds a large amount of unprocessed data that resides very crucial information. A single pair of chromosomes contains approximately 3 billion dna base pairs. To look through this information, retrieve the connections, and subconnections in it is a very slow procedure. therefore, scientists are looking forward toward computer science algorithms for faster retrieval of information. this paper is focused upon using a parallel programming algorithm than the previous alignment algorithms.

关键词： dna Genetics Parallel algorithms thread

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Agarose droplet microfluidic approach for molecular evolution of aptamers

Agarose droplet microfluidic approach for molecular evolutio...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Zhang, Wenhua Zhang, Weiyun Liu, Zhiyuan Li, Cong Jenkins, Gareth Yang, Chaoyong James Department of Chemical Biology Xiamen University Xiamen 361005 China

ISBN: (纸本)9781618395955

We have developed a novel method for efficient screening of affinity ligands (aptamers) from a complex single-stranded dna (ssdna) library by employing single molecule emulsion PCR based on agarose droplet microfluidic technology . Statistically diluted ssdna of a pre-enriched library was encapsulated into individual uniform agarose droplets for highly efficient single molecule emulsion PCR to generate clonal agarose beads. the binding affinity of amplified ssdna from each clonal agarose bead was tested via high-throughput flow cytometry. dna clones with high binding affinity and low dissociation constant (Kd) were chosen as potential aptamers and can be directly used for downstream biomedical applications. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： dna

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dna sequence visualization and feature extraction

DNA sequence visualization and feature extraction

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15th World Multi-conference on Systemics, Cybernetics and Informatics, WMSCI 2011

作者： Trifas, Monica Francia III, Guillermo Murdock, Chris Mann, Crystal Mayo, Quention Wiggins, Ashley Department of Mathematical Computing and Information Sciences Jacksonville State University 700 Pelham Road N. Jacksonville AL 36265 United States Department of Biology Jacksonville State University 700 Pelham Road N. Jacksonville AL 36265 United States

ISBN: (纸本)9781936338306

the 2010-2011 Jacksonville State University (JSU)-CREU project's focus is on problems in the area of dna sequence visualization. Specialized software (BLAST, FASTA, etc) are utilized for identifying and aligning nucleotide sequences obtained from sample data provided by the Biology department at JSU. the project team designed and implemented a visualization system that takes, as input, the output of the specialized dna-analysis software. the output of the visualization system is a visual display of the text-formatted input data. To complete the JSU-CREU project, biology students will be asked to complete a survey on the usability of this and other visualization systems. the results of the survey will be statistically analyzed and an analysis report will be written.

关键词： dna sequences

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dna computing and molecular programming: Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2009年 5877 LNCS卷

作者： Deaton, Russell Suyama, Akira Dept. of Computer Science and Computer Engineering JBHT - CSCE 504 1 University of Arkansas Fayetteville AR 72701 United States Department of Life Science Graduate School of Arts and Sciences University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

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Proceedings - 2017 IEEE 15th international conference on Dependable, Autonomic and Secure computing, 2017 IEEE 15th international conference on Pervasive Intelligence and computing, 2017 IEEE 3rd

Proceedings - 2017 IEEE 15th International Conference on Dep...

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15th IEEE international conference on Dependable, Autonomic and Secure computing, 2017 IEEE 15th international conference on Pervasive Intelligence and computing, 2017 IEEE 3rd international conference on Big Data Intelligence and computing and 2017 IEEE Cyber Science and Technology Congress, DASC-PICom-DataCom-CyberSciTec 2017

ISBN: (纸本)9781538619551

the proceedings contain 203 papers. the topics discussed include: semantic neuron networks based associative memory model;an integrative and precise approach in personality computing based on ontic personae modeling;deep convolution neural network discriminator for distinguishing seborrheic keratosis and flat warts;pairwise preference over mixed-type item-sets based Bayesian personalized ranking for collaborative filtering;design considerations for cyber security testbeds: a case study on a cyber security testbed for education;detecting Android malware based on extreme learning machine;a survey of semantics-aware performance optimization for data-intensive computing;identifying image tags from Instagram hashtags using the HITS algorithm;caching scheme with edge nodes for mobile cyber physical systems;a study on communication network reliability for advanced metering infrastructure in smart grid;interference management for physical layer security in heterogeneous networks;a real example of Jong Nang and tomb gate of cyber biology Jeju island: its fundamental principle of dna code;MMHG: multi-modal hypergraph learning for overall survival after D2 gastrectomy for gastric cancer;respiratory sounds feature learning with deep convolutional neural networks;a bus arrival time prediction method based on GPS position and real-time traffic flow;and re-thinking online offenders' SKRAM: individual traits and situational motivations as additional risk factors for predicting cyber attacks.

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EWOD based microfluidic system with coplanar electrodes for parallel dna ligation of ultramicro volume

EWOD based microfluidic system with coplanar electrodes for ...

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TRANSDUCERS 2009 - 15th international conference on Solid-State Sensors, Actuators and Microsystems

作者： Lin, H.C. Liu, Y.J. Yao, D.J. Chang, H.Y. Institute of NanoEngineering and MicroSystems National Tsing Hua University Hsinchu Taiwan Institute of Molecular Medicine National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)9781424441938

this paper reports the completion of a parallel ultramicro-volume dna ligation processes using a coplanar electrode type of electrowetting-on- dielectric (EWOD) microfluidic system. the droplets, containing dna, a ligation enzyme and a multi-salt reaction buffer, served to complete the ligation using a developed EWOD system. In order to reduce the effect from environment, so the concept of core-shell droplet was used in this study. Droplets of ultramicro volume (0.3L) were successfully generated from reservoirs between one plate with coplanar electrodes and another plate with a hydrophobic surface free of electrodes. In one successful cloning, the total usage of reagents in an ultramicro-volume EWOD chip was 2.1L;no volume was wasted, in comparison with 85% waste with the standard protocol (15L). the results also show that the four parallel dna ligation processes were accomplished without damage to the chip surface and without biomaterial annulment. ©2009 IEEE.

关键词： Drops

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Antigenic Epitope prediction of small envelope protein and designing a vaccine by using Reverse vaccinology approach against SARS Coronavirus Tor2 strain

Antigenic Epitope prediction of small envelope protein and d...

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15th international conference on Advanced computing Technologies (ICACT)

作者： Kumar, Amit Bhattacharya, Anupam Kashyap, Amita BioAxis DNA Res Ctr P Ltd Hyderabad Andhra Pradesh India

ISBN: (纸本)9781467328166;9781467328180

Severe acute respiratory syndrome (SARS) is a serious form of pneumonia which results in acute respiratory distress and sometimes death. In this study, we applied the reverse vaccinology approach to determine the antigenic determinant sites present on the protein. the method incorporates the prediction of antigenic sites, solvent accessible region and secondary structure, B-cell epitope prediction, and the designing of antigenic determinant. the results of the study suggested that small envelope protein and orf8 protein could be potential candidates for vaccine designing. the high scoring antigenic peptides were designed and optimized. It is inferred that peptide of small envelope protein will make a very stable and effective vaccine targeting the E protein of the virus which is responsible for the spread of the virion. this study provides a strong and a potential optimized vaccine against SARS, which has high chances of success of immunization and higher probabilities of combating the dreadful disease.

关键词： SARS small envelope protein Vaccine design antigen prediction Epitope prediction reverse vaccinology

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